Topic · Gene Regulatory Network Analysis
Most cited papers in Gene Regulatory Network Analysis
What are the most cited papers in Gene Regulatory Network Analysis?
The most cited paper in Gene Regulatory Network Analysis is "Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks" (Paul T. Shannon, Andrew Markiel, Owen W. Ozier et al., 2003), with 55,788 citations. Next come "edgeR : a Bioconductor package for differential expression analysis of digital gene expression data" (45,449) and "Collective dynamics of ‘small-world’ networks" (43,707).
Showing 50 of 99 papers. Every paper with more than 1,725 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Paul T. Shannon, Andrew Markiel, Owen W. Ozier et al. · Genome Research | Nov 2003 | 55,788 |
| 2 | edgeR : a Bioconductor package for differential expression analysis of digital gene expression data Mark D. Robinson, Davis James McCarthy, Gordon K. Smyth · Bioinformatics | 11 Nov 2009 | 45,449 |
| 3 | Collective dynamics of ‘small-world’ networks Duncan J. Watts, Steven H. Strogatz · Nature | Jun 1998 | 43,707 |
| 4 | Complex networks: Structure and dynamics Stefano Boccaletti, Vito Latora, Yamir Moreno et al. · Physics Reports | 11 Jan 2006 | 11,156 |
| 5 | Enzymatic assembly of DNA molecules up to several hundred kilobases Daniel G. Gibson, Lei Young, Ray-Yuan Chuang et al. · Nature Methods | 12 Apr 2009 | 11,139 |
| 6 | SCANPY: large-scale single-cell gene expression data analysis F. Alexander Wolf, Philipp Angerer, Fabian Joachim Theis · Genome biology | 6 Feb 2018 | 9,901 |
| 7 | Exploring complex networks Steven H. Strogatz · Nature | Mar 2001 | 8,412 |
| 8 | Network biology: understanding the cell's functional organization Albert-Ĺaszló Barabási, Zoltán N. Oltvai · Nature Reviews Genetics | 21 Jan 2004 | 8,151 |
| 9 | Massively parallel digital transcriptional profiling of single cells Grace X. Y. Zheng et al. · Nature Communications | 16 Jan 2017 | 8,144 |
| 10 | Spatial reconstruction of single-cell gene expression data Rahul Satija, Jeffrey A. Farrell, David G. Gennert et al. · Nature Biotechnology | 13 Apr 2015 | 8,018 |
| 11 | Network Motifs: Simple Building Blocks of Complex Networks Ron Milo, Shai S. Shen-Orr, Shalev Itzkovitz et al. · Science | 24 Oct 2002 | 7,594 |
| 12 | SCENIC: single-cell regulatory network inference and clustering Sara Aibar, Carmen Bravo González‐Blas, Thomas Moerman et al. · Nature Methods | 9 Oct 2017 | 7,321 |
| 13 | The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling Konstantin Arnold, Lorenza Bordoli, Jürgen Kopp et al. · Bioinformatics | 13 Nov 2005 | 7,119 |
| 14 | A General Framework for Weighted Gene Co-Expression Network Analysis Bin Zhang, Steve Horvath · Statistical Applications in Genetics and Molecular Biology | 12 Jan 2005 | 6,132 |
| 15 | Stochastic Gene Expression in a Single Cell Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia et al. · Science | 16 Aug 2002 | 5,801 |
| 16 | Reversed graph embedding resolves complex single-cell trajectories Xiaojie Qiu, Qi Rong Mao, Ying Tang et al. · Nature Methods | 21 Aug 2017 | 5,638 |
| 17 | The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease Justin Lamb, Emily D. Crawford, David D. Peck et al. · Science | 28 Sep 2006 | 5,546 |
| 18 | Network medicine: a network-based approach to human disease Albert-Ĺaszló Barabási, Natali Gulbahce, Joseph Loscalzo · Nature Reviews Genetics | 17 Dec 2010 | 5,228 |
| 19 | A synthetic oscillatory network of transcriptional regulators Michael B. Elowitz, Stanislas Leibler · Nature | 2000 | 4,810 |
| 20 | Maps of random walks on complex networks reveal community structure Martin Rosvall, Carl T. Bergstrom · Proceedings of the National Academy of Sciences | 23 Jan 2008 | 4,772 |
| 21 | Molecular Computation of Solutions to Combinatorial Problems Leonard M. Adleman · Science | 11 Nov 1994 | 4,482 |
| 22 | Construction of a genetic toggle switch in Escherichia coli Timothy S. Gardner, Charles R. Cantor, James J. Collins · Nature | 2000 | 4,468 |
| 23 | Systems Biology: A Brief Overview Hiroaki Kitano · Science | Mar 2002 | 4,305 |
| 24 | What is flux balance analysis? Jeffrey D. Orth, Ines Thiele, Bernhard Ørn Palsson · Nature Biotechnology | Mar 2010 | 4,197 |
| 25 | Mean shift, mode seeking, and clustering Yizong Cheng · IEEE Transactions on Pattern Analysis and Machine Intelligence | 1995 | 3,912 |
| 26 | Fast gene set enrichment analysis Gennady Korotkevich, Vladimir Sukhov, Nikolay Budin et al. · bioRxiv (Cold Spring Harbor Laboratory) | 20 Jun 2016 | 3,771 |
| 27 | Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells Allon Moshe Klein, Linas Mažutis, Ilke Akartuna et al. · Cell | May 2015 | 3,759 |
| 28 | From molecular to modular cell biology Leland H. Hartwell, J. J. Hopfield, Stanislas Leibler et al. · Nature | 2 Dec 1999 | 3,729 |
| 29 | MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data Greg Finak, Andrew McDavid, Masanao Yajima et al. · Genome biology | Dec 2015 | 3,705 |
| 30 | Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics Kelly Street, Davide Risso, Russell B. Fletcher et al. · BMC Genomics | 18 Jun 2018 | 3,551 |
| 31 | The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Ron Caspi, Richard Billington, Luciana Ferrer et al. · Nucleic Acids Research | 2 Nov 2015 | 3,528 |
| 32 | Network motifs: theory and experimental approaches Uri S. Alon · Nature Reviews Genetics | 18 May 2007 | 3,473 |
| 33 | Controllability of complex networks Yang‐Yu Liu, Jean-Jacques E. Slotine, Albert-Ĺaszló Barabási · Nature | May 2011 | 3,341 |
| 34 | Using Bayesian Networks to Analyze Expression Data Nir Friedman, Michal Linial, Iftach Nachman et al. · Journal of Computational Biology | Aug 2000 | 3,337 |
| 35 | The human disease network K.-I. Goh, Michael E. Cusick, David Valle et al. · Proceedings of the National Academy of Sciences | 14 May 2007 | 3,284 |
| 36 | Generalizing RNA velocity to transient cell states through dynamical modeling Volker Bergen, Marius Lange, Stefan Peidli et al. · Nature Biotechnology | 3 Aug 2020 | 3,233 |
| 37 | The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Michael Hucka et al. · Bioinformatics | 28 Feb 2003 | 3,190 |
| 38 | Specificity and Stability in Topology of Protein Networks Sergei Maslov, Kim Sneppen · Science | 3 May 2002 | 3,152 |
| 39 | Java Treeview—extensible visualization of microarray data Alok J. Saldanha · Bioinformatics | 4 Jun 2004 | 3,133 |
| 40 | A methodology for performing global uncertainty and sensitivity analysis in systems biology Simeone Marino, Ian B. Hogue, Christian J. Ray et al. · Journal of Theoretical Biology | 21 Apr 2008 | 3,092 |
| 41 | Biomimicry of bacterial foraging for distributed optimization and control Kevin M. Passino · IEEE Control Systems | Jun 2002 | 3,082 |
| 42 | Network motifs in the transcriptional regulation network of Escherichia coli Shai S. Shen-Orr, Ron Milo, Shmoolik Mangan et al. · Nature Genetics | 22 Apr 2002 | 3,075 |
| 43 | Transcriptional Regulatory Networks in Saccharomyces cerevisiae Tong Ihn Lee et al. · Science | 24 Oct 2002 | 3,022 |
| 44 | Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences Arjun Raj, Alexander van Oudenaarden · Cell | Oct 2008 | 2,824 |
| 45 | COPASI—a COmplex PAthway SImulator Stefan Hoops, Sven Sahle, Ralph Gauges et al. · Bioinformatics | 10 Oct 2006 | 2,743 |
| 46 | Modeling and Simulation of Genetic Regulatory Systems: A Literature Review Hidde de Jong · Journal of Computational Biology | 2002 | 2,705 |
| 47 | Improvements to the APBS biomolecular solvation software suite Elizabeth R. Jurrus et al. · Protein Science | 24 Aug 2017 | 2,626 |
| 48 | Variance stabilization applied to microarray data calibration and to the quantification of differential expression Wolfgang K. Huber, Anja von Heydebreck, Holger Sültmann et al. · Bioinformatics | Jul 2002 | 2,619 |
| 49 | Integration of biological networks and gene expression data using Cytoscape Melissa Cline et al. · Nature Protocols | 27 Sep 2007 | 2,601 |
| 50 | ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context Adam A Margolin, Ilya Nemenman, Katia Basso et al. · BMC Bioinformatics | Mar 2006 | 2,525 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.